Ok, sorry for the long time since an update.. I recently got the spindle problem fixed! I think that when the machine fell on its face, the spindle/backplate interface got bent. I was able to correct this by facing off the entire chuck backplate and re-creating the chuck interface. I can now get VERY good consistency, under a thou - if I spend the time to get the part tapped in, in the 3-jaw that I currently have. While doing this, my cross-slide nut broke, so I went and got some Grizzly.com parts.. I replaced the nut, the lead screw(it was bent), and the bracket(broken, and had cobbled something together).. it all fit perfectly, though the nut WAS different enough to be concerning upon inspection... all at a fraction of the JET prices, too.. so that's a great tip!
Other things I have completed:
Putting fresh bearings on the spindle and pressing them on.
"Quick and dirty" headstock alignment, using a shim to just align it to the ways.
Rebuild of the cross-slide assembly and replacement of broken and improvised parts.
I was able to purchase a little HiTorque Mini Mill off of LittleMachineShop.
Anyway, I was able to solve the problem I couldn't get past thanks to the help here, so THANK YOU everybody, your help and advice have been invaluable!